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Series GSE252124 Query DataSets for GSE252124
Status Public on Apr 27, 2024
Title Discovery of Varicella zoster virus circular RNA with nanopore long-read sequencing
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Varicella-zoster virus (VZV), an alphaherpesvirus, causes chickenpox (varicella) in young children with an annual minimum of 140 million new cases and herpes zoster in senior, a painful and debilitating disease with 3-5‰ incidence. A complex structural transcriptome of VZV, which numerous novel transcripts, transcript isoforms, and unknown splice events are found during cell infection. Circular RNA (circRNA), a newly important component of the transcriptome, is increasing discoveries of circRNA function in mammalian cells. However, VZV encoded circRNA remains unexplored. The code used in this study and extended data are available from the GitHub repository (https://github.com/ShaominYang/VZV_circRNA)
 
Overall design Using deep RNA-seq following RNase R treatment, we identified and charactered 35, 076 and 54 human and VZV pOka strain circRNAs respectively from VZV infected neuroblastoma cell (SH-SY5Y). We collected VZV infected human neuroblastoma cell (SH-SY5Y). A deep nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing following RNase R treatment was performed.
Web link https://www.nature.com/articles/s41467-024-49112-4
 
Contributor(s) Yang S
Citation(s) 38858365
Submission date Dec 27, 2023
Last update date Jun 11, 2024
Contact name SHAO MIN YANG
E-mail(s) shaominyang@stu2020.jnu.edu.cn
Organization name Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine
Department Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center
Street address Nanshan
City Shenzhen
State/province guangdong
ZIP/Postal code 518060
Country China
 
Platforms (1)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (1)
GSM7994749 circRNA long reads sequencing
Relations
BioProject PRJNA1057831

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE252124_RAW.tar 140.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA

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